What does a Global Fish Community Time-series Database Tell us about Biodiversity Trends in Freshwater Environments?

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.title[
# What does a Global Fish Community Time-series Database Tell us about Biodiversity Trends in Freshwater Environments?
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.subtitle[
## Joint Aquatic Sciences Meeting 2022
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.author[
### <strong>Alain Danet</strong>, Xingli Giam, Julian Olden, Lise Comte
]
.author[
### Illinois State University
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.author[
### <a href="https://alaindanet.github.io">https://alaindanet.github.io</a>
]
.date[
### Slides created via the R package <a href="https://github.com/yihui/xaringan">xaringan</a>
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# Biodiversity in crisis

.footnote[[Newbold, et al. (2015)](https://www.nature.com/articles/nature14324); [IPBES, (2019)](https://ipbes.net/sites/default/files/2020-02/ipbes_global_assessment_report_summary_for_policymakers_fr.pdf), [Image credit: UNEP](https://production-wordpress.unep-wcmc.org/content//uploads/2021/11/Bending-the-Curve_PR.jpg)]

???
Scientists reach a consensus on the fact that biodiversity is going through an
unprecedented crisis. Predictions indicates that if we do not act strongly and
quickly, this crisis could have dramatic consequences that have not been seen
yet.

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# Freshwater fishes

.footnote[[He, et al. (2017)](https://onlinelibrary.wiley.com/doi/abs/10.1002/wat2.1208); [Reid, et al. (2019a)](https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12480); [IPBES, (2019)](https://ipbes.net/sites/default/files/2020-02/ipbes_global_assessment_report_summary_for_policymakers_fr.pdf)]

???
This is particularly true for freshwater ecosystems. Although freshwater
constitute 0.01% of water on earth, they host almost 9.5% of Earth described
species. Freshwater biodiversity is threatened by terrestrial land degradation,
overexploitation, pollution, flow alteration and species alteration.

However we know little on temporal dynamics of freshwater fishes are affected by
those anthropogenic pressures.

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# Describing biodiversity changes

.footnote[Image: [worldwildlife.org](https://files.worldwildlife.org/wwfcmsprod/images/Buffalo_fish/story_full_width/80b2nhfpi6_Buffalo_fish__c__Freshwaters_Illustrated.jpg)]

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## Multidimensional concept

1. Species richness
1. Total abundance
1. Dissimilarity in species composition (P/A or abundance based)

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???
When an ecologist sampled a community in time, he faces a difficult task. Indeed, how to
describe the trends in biodiversity of this community?

Is it the number of species, the total abundance, the dissimilarity of the
community composition through time? Should I take in account the abundance of
the species, in other word, compute Hill numbers ?

Of course, this is no one good answer. But measuring several of them, when
possible, can help us to refine our understanding biodiversity changes.  
An alternative hypothesis is that biodiversity trends are similar among them,
and that we might need only a few.

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# Research questions

How do anthropogenic pressures influence the temporal trends of freshwater fish
biodiversity?

Do different biodiversity facets have the same temporal trends?

???
Regarding the previous research gap, we asked
"How do anthropogenic pressures influence the temporal trends of freshwater fish
biodiversity?" and

"Do different biodiversity facets have the same temporal trends?"

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#

Methods

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# Fish data: RivFishTime

5359 sites, spanning at least 10 years

Homogeneity within sites: protocol, abundance units, sampling period

.footnote[[Comte, et al. (2021)](https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13210)]

???
To answer those questions, we used the RivFishTime database which contains time
series of fish communities spanning at least 10 years. The dataset covers mostly
the so called "Western countries": the US and Canada, Western and North Europe,
Australia and Japan. For each site, we selected samplings that were identical in
terms of protocol, measurement unit and sampling season. 
After selection, we had more than 5000 sites.

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# Biodiversity facets

## Temporal dissimilarity:
- Simpson based dissimilarity
- Jaccard (Presence / absence):
  - Appearance and Disappearance 
  - Turnover and Nestedness

## Species richness and total abundance:
- Chao species richness
- Total abundance

## Complementary descriptors: exotic species
- Percentage of exotic species richness 
- Percentage of exotic species abundance

???
We characterised biodiversity by temporal dissimilarity of community
composition: based on abundance (with Simpson), presence/absence with the
Jaccard index. We also decomposed Jaccard in Appearance/Disappearance and
Nestedness/Turnover

We also described the Coverage based species richness (the Chao) and Total
abundance.

We also described the composition of communities in terms of exotic species

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# Anthropogenic pressures

## Human footprint (1993; 2009)

Based on human infrastructures, land-use, population density

.footnote[[Venter, et al. (2016b)](https://www.nature.com/articles/ncomms12558)]

???
We described anthropogenic pressures using the Human Footprint index. It is a
composite index that take in account human infrastructures, land-use,
and various characteristics of human occupation.